DiffExplore

library(dplyr)
library(lubridate)
library(zoo)
library(ggplot2)
library(limma)
library(ggpubr)
library(grid)
library(plotly)

#Data Files and prep work
source("../../lib/DataProccess.R")
source("../../lib/NormFuncs.R")
source("../../lib/OutlierDetectionFuncs.R")
source("../../lib/DataPathName.R")
BaseDir <- params$BaseDir#get the root of the directory where the data is stored

“Files Used:”

COVID-19_WastewaterAnalysis/data/processed/LIMSWasteData_02-09-22.csv

RankingDF <- LIMSFullDF%>%
  #filter(Date<mdy("10/31/2021"))%>%
  #group_by(Site)%>%
  arrange(Date)%>%
  mutate(N1 = ifelse(!is.na(N1),N1,0))%>%
  mutate(N2 = ifelse(!is.na(N2),N2,0))%>%
  mutate(N1RankLeft = rank(desc(N1 - lag(N1))),
         N1RankRight = rank(desc(N1 - lead(N1))),
         N2RankLeft = rank(desc(N2 - lag(N2))),
         N2RankRight = rank(desc(N2 - lead(N2))))%>%
  select(Date,Site,N1RankLeft,N1RankRight,N2RankLeft,N2RankRight,N1,N2)%>%
  mutate(MaxN1Rank = -pmax(N1RankLeft,N1RankRight,N2RankLeft,N2RankRight))


BreakUsed <- c(.90,.95)
Vec <- PlotlyView(RankingDF, "MaxN1Rank", QuintileBound, Threshold = BreakUsed)
Vec[[1]]

Vec[[2]]

RankingDF%>%
  filter(-MaxN1Rank<=10)%>%
  arrange(Date,Site)

    #Instead Max 10, Max 20
  #Rolling SD Vs Rolling mean
  
  #1) Show everthing for clear outliers
  #2) Show soft with 25

Vec[[3]]%>%
  arrange(FlagScheme)%>%
  #select(-)%>%
  rename(ErrorLevel = FlagScheme, Rank = `MaxN1Rank`)%>%
  mutate(Rank = -Rank)%>%
  arrange(ErrorLevel, Rank)#%>%

  #write.csv("RmdOutput/PossibleOutliers.csv")

ThresholdFlagDF <- RankingDF%>%
  mutate(ThresholdOutlier= -MaxN1Rank<=12)%>%
  arrange(Date,Site)%>%
    ggplot(aes(x = Date))+
    theme(panel.spacing.y = unit(2, "lines"))+
    geom_point(aes(y = N1, color = Site, shape = "N1", info = -MaxN1Rank,
                   alpha = ThresholdOutlier, size = ThresholdOutlier))+
  geom_point(aes(y = N2, color = Site, shape = "N2", info = -MaxN1Rank,
                   alpha = ThresholdOutlier, size = ThresholdOutlier))
  GGPlotlyWithScaling(ThresholdFlagDF,2, Display = c("N1","N2", "Date", "info"))

ThresholdFlagDF <- RankingDF%>%
  mutate(MaxN1Rank = -MaxN1Rank, ThresholdOutlier = ifelse(MaxN1Rank<=47,"BFlagged","ANotFlagged"),
         ThresholdOutlier= ifelse(MaxN1Rank<=12, "CFlaggedRestrictive", ThresholdOutlier))%>%
  arrange(Date,Site)%>%
    ggplot(aes(x = Date))+
    theme(panel.spacing.y = unit(1, "lines"))+
    geom_point(aes(y = N1, color = ThresholdOutlier, shape = "N1",
                   alpha = ThresholdOutlier, size = ThresholdOutlier, info = MaxN1Rank))+
  geom_point(aes(y = N2, color = ThresholdOutlier, shape = "N2",
                   alpha = ThresholdOutlier, size = ThresholdOutlier, info = MaxN1Rank))+
  facet_wrap(~Site, ncol = 1, scales = "free")

  GGPlotlyWithScaling(ThresholdFlagDF,3, Display = c("N1","N2", "Date", "info"))